Daphnia species have becomemodels for ecological genomics and exhibit interesting features, such as high phenotypic plasticity andadenselypackedgenome withmany lineage-specificgenes. They are also cyclicparthenogenetic, withalternatingasexual and sexual cycles and environmental sex determination. Here, wepresent a de novo transcriptomeassembly of over 32,000 D. galeata genesanduse it to investigategene expressionin females andspontaneously producedmalesof twoclonal lines derivedfromlakes in Germany and the Czech Republic.We find that only a low percentage (18%) of genes shows sex-biased expression and that there are many more female-biased gene (FBG) than male-biased gene (MBG). Furthermore, FBGs tend to be more conserved between species than MBGs in both sequence and expression. These patterns may be a consequence of cyclic parthenogenesis leading to a relaxation of purifying selection on MBGs. The two clonal lines show considerable differences in both number and identity of sex-biased genes, suggesting that they may have reproductive strategies differing in their investment in sexual reproduction. Orthologs of key genes in the sex determination and juvenile hormone pathways,which are thought to be important for the transition from asexual to sexual reproduction, are present in D. galeata and highly conserved among Daphnia species.